# Bio.Phylo.PhyloXMLIO module

PhyloXML reader/parser, writer, and associated functions.

Instantiates tree elements from a parsed PhyloXML file, and constructs an XML file from a `Bio.Phylo.PhyloXML` object.

About capitalization:

  - phyloXML means the file format specification

  - PhyloXML means the Biopython module `Bio.Phylo.PhyloXML` and its classes

  - Phyloxml means the top-level class used by `PhyloXMLIO.read` (but not `Bio.Phylo.read`!), containing a list of Phylogenies (objects derived from `BaseTree.Tree`)

exception Bio.Phylo.PhyloXMLIO.PhyloXMLError

  Bases: `Exception`

  Exception raised when PhyloXML object construction cannot continue.

  XML syntax errors will be found and raised by the underlying ElementTree module; this exception is for valid XML that breaks the phyloXML specification.

  __firstlineno__ = 39
  __static_attributes__ = ()

Bio.Phylo.PhyloXMLIO.read(file)

  Parse a phyloXML file or stream and build a tree of Biopython objects.

  The children of the root node are phylogenies and possibly other arbitrary (non-phyloXML) objects.

  Returns:

    a single `Bio.Phylo.PhyloXML.Phyloxml` object.

Bio.Phylo.PhyloXMLIO.parse(file)

  Iterate over the phylogenetic trees in a phyloXML file.

  This ignores any additional data stored at the top level, but may be more memory-efficient than the `read` function.

  Returns:

    a generator of `Bio.Phylo.PhyloXML.Phylogeny` objects.

Bio.Phylo.PhyloXMLIO.write(obj, file, encoding=DEFAULT_ENCODING, indent=True)

  Write a phyloXML file.

  Parameters:
    obj

      an instance of `Phyloxml`, `Phylogeny` or `BaseTree.Tree`, or an iterable of either of the latter two. The object will be converted to a Phyloxml object before serialization.

    file

      either an open handle or a file name.

class Bio.Phylo.PhyloXMLIO.Parser(file)

  Bases: `object`

  Methods for parsing all phyloXML nodes from an XML stream.

  To minimize memory use, the tree of ElementTree parsing events is cleared after completing each phylogeny, clade, and top-level ‘other’ element. Elements below the clade level are kept in memory until parsing of the current clade is finished – this shouldn’t be a problem because clade is the only recursive element, and non-clade nodes below this level are of bounded size.

  __init__(file)

    Initialize the class.

  read()

    Parse the phyloXML file and create a single Phyloxml object.

  parse()

    Parse the phyloXML file incrementally and return each phylogeny.

  other(elem, namespace, localtag)

    Create an Other object, a non-phyloXML element.

  accession(elem)

    Create accession object.

  annotation(elem)

    Create annotation object.

  binary_characters(elem)

    Create binary characters object.

  clade_relation(elem)

    Create clade relationship object.

  color(elem)

    Create branch color object.

  confidence(elem)

    Create confidence object.

  date(elem)

    Create date object.

  distribution(elem)

    Create geographic distribution object.

  domain(elem)

    Create protein domain object.

  domain_architecture(elem)

    Create domain architecture object.

  events(elem)

    Create events object.

  id(elem)

    Create identifier object.

  mol_seq(elem)

    Create molecular sequence object.

  point(elem)

    Create point object, coordinates of a point.

  polygon(elem)

    Create polygon object, list of points.

  property(elem)

    Create properties from external resources.

  reference(elem)

    Create literature reference object.

  sequence_relation(elem)

    Create sequence relationship object, relationship between two sequences.

  uri(elem)

    Create uri object, expected to be a url.

  __firstlineno__ = 263
  __static_attributes__ = ('context', 'root')

class Bio.Phylo.PhyloXMLIO.Writer(phyloxml)

  Bases: `object`

  Methods for serializing a PhyloXML object to XML.

  __init__(phyloxml)

    Build an ElementTree from a PhyloXML object.

  write(file, encoding=DEFAULT_ENCODING, indent=True)

    Write PhyloXML to a file.

  phyloxml(obj)

    Convert phyloxml to Etree element.

  other(obj)

    Convert other to Etree element.

  phylogeny(obj)

    Serialize a phylogeny and its subnodes, in order.

  clade(obj)

    Serialize a clade and its subnodes, in order.

  accession(obj)

    Serialize a accession and its subnodes, in order.

  annotation(obj)

    Serialize a annotation and its subnodes, in order.

  binary_characters(obj)

    Serialize a binary_characters node and its subnodes.

  clade_relation(obj)

    Serialize a clade_relation and its subnodes, in order.

  color(obj)

    Serialize a color and its subnodes, in order.

  confidence(obj)

    Serialize a confidence and its subnodes, in order.

  date(obj)

    Serialize a date and its subnodes, in order.

  distribution(obj)

    Serialize a distribution and its subnodes, in order.

  domain(obj)

    Serialize a domain node.

  domain_architecture(obj)

    Serialize a domain_architecture and its subnodes, in order.

  events(obj)

    Serialize a events and its subnodes, in order.

  id(obj)

    Serialize a id and its subnodes, in order.

  mol_seq(obj)

    Serialize a mol_seq and its subnodes, in order.

  node_id(obj)

    Serialize a node_id and its subnodes, in order.

  point(obj)

    Serialize a point and its subnodes, in order.

  polygon(obj)

    Serialize a polygon and its subnodes, in order.

  property(obj)

    Serialize a property and its subnodes, in order.

  reference(obj)

    Serialize a reference and its subnodes, in order.

  sequence(obj)

    Serialize a sequence and its subnodes, in order.

  sequence_relation(obj)

    Serialize a sequence_relation and its subnodes, in order.

  taxonomy(obj)

    Serialize a taxonomy and its subnodes, in order.

  uri(obj)

    Serialize a uri and its subnodes, in order.

  alt(obj)

    Serialize a simple alt node.

  branch_length(obj)

    Serialize a simple branch_length node.

  lat(obj)

    Serialize a simple lat node.

  long(obj)

    Serialize a simple long node.

  maximum(obj)

    Serialize a simple maximum node.

  minimum(obj)

    Serialize a simple minimum node.

  value(obj)

    Serialize a simple value node.

  width(obj)

    Serialize a simple width node.

  blue(obj)

    Serialize a simple blue node.

  duplications(obj)

    Serialize a simple duplications node.

  green(obj)

    Serialize a simple green node.

  losses(obj)

    Serialize a simple losses node.

  red(obj)

    Serialize a simple red node.

  speciations(obj)

    Serialize a simple speciations node.

  bc(obj)

    Serialize a simple bc node.

  code(obj)

    Serialize a simple code node.

  common_name(obj)

    Serialize a simple common_name node.

  desc(obj)

    Serialize a simple desc node.

  description(obj)

    Serialize a simple description node.

  location(obj)

    Serialize a simple location node.

  name(obj)

    Serialize a simple name node.

  rank(obj)

    Serialize a simple rank node.

  scientific_name(obj)

    Serialize a simple scientific_name node.

  symbol(obj)

    Serialize a simple symbol node.

  synonym(obj)

    Serialize a simple synonym node.

  type(obj)

    Serialize a simple type node.

  __firstlineno__ = 710
  __static_attributes__ = ('_tree',)

Biopython v: 1.85

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